Beach Ball after Startup or Hibernation

Greetings,
I face a very annoying problem and I have no idea how to troubleshoot. Most of the time, when I start the computer or wake it up, I get a beach ball for 2-5 minutes. It doesn't happen all the time but when it does, nothing responds except GUI. It doesn't occur immediately but after 3-5 minutes of regular usage. I can't pinpoint it to a single application. I saw beach ball after starting or using iTunes, starting Skype, opening a few tabs in Firefox, executing a MySQL query and so on. It happens only once per session and everything is fine after that until I shut down or put the computer to sleep.
I tried to run top but it freezes before I can see which process jumps to the top.
Also, in the console I saw "kernel[0]: jnl: unknown-dev: flushing fs disk buffer returned 0x5". But it's not there after each beach ball. So, I don't know if it's related or not.
Finally, I suspect it started after I enabled "put the hard disks to sleep when possible". I tried that option on and off and in different combinations for Battery and Power Adapter, it doesn't solve the problem.
I would appreciate any help. The issue drives me absolutely nuts.
Thanks!

I only have Logitech Trackman connected from time to time and I get beach ball with or without it.
I was able to re-create the problem and dumped the messages. Only two of them look suspicious.
Nov 12 21:52:36 localhost kernel[0]: GFX0: family specific matching fails
Nov 12 21:52:50 leleka kernel[0]: AppleYukon2: 00000000,00000000 sk98osx_dnet - recovering from missed interrupt
They were well before the beach ball, which occurred at 22:02 and lasted for 3 minutes. I reviewed all log files and there are absolutely no messages from 21:53 to 22:05 when beach ball was over and I opened a terminal window.
There are a few error messages in system.log that are most likely unrelated as well.
Nov 12 21:53:08 leleka mDNSResponder[22]: NOTE: Wide-Area Service Discovery disabled to avoid crashing defective DNS relay 192.168.78.1:53
Nov 12 21:53:08 leleka Dock[112]: _DESCRegisterDockExtraClient failed 268435459
Nov 12 21:53:09 leleka loginwindow[23]: Unable to resolve startup item: status = -36, theURL == NULL = 1
Nov 12 21:53:09 leleka loginwindow[23]: Unable to resolve startup item: status = -43, theURL == NULL = 1
I have VMWare installed. I don't currently use it but it does a lot of work at startup. Perhaps, I should try uninstalling it?
Thanks!

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